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. 1984 Jul 25;12(14):5913–5925. doi: 10.1093/nar/12.14.5913

The Raman spectra of left-handed DNA oligomers incorporating adenine-thymine base pairs+.

J M Benevides, A H Wang, G A van der Marel, J H van Boom, A Rich, G J Thomas Jr
PMCID: PMC320040  PMID: 6462921

Abstract

Raman spectra were obtained from single crystals of [d(CGCATGCG)]2 and [d(m5CGTAm5CG)]2, both of which incorporate A-T pairs into Z-DNA structures and contain C2'-endo/syn conformers of deoxyguanosine at the oligonucleotide ends. Correlation with x-ray results permits the following Raman assignments for nucleoside conformers: C3'-endo/syn G, 623 +/- 1; C2'-endo/syn G, 671 +/- 2; C2'-endo/anti C, 782 +/- 1; C2'endo/anti T, 650 +/- 5 and ca. 750; C3'-endo/syn A, 729 +/- 1 cm-1. These results show that (i) the 670 cm-1 line of syn G is highly sensitive to the change from C3'-endo to C2'-endo pucker, (ii) the 729 cm-1 line of A is affected neither by furanose pucker nor glycosidic bond orientation and (iii) the 1200-1500 cm-1 region of the Raman spectrum of the A-T double helix is greatly altered by the B-to-Z transition. Conformation sensitive Raman frequencies in the 850-1700 cm-1 region are identified for both octamer and hexamer, and the Z-to-B transition of each is monitored by spectral changes which occur upon dissolving the crystal in H2O solution.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Benevides J. M., Lemeur D., Thomas G. J., Jr Molecular conformations and 8-CH exchange rates of purine ribo- and deoxyribonucleotides: investigation by Raman spectroscopy. Biopolymers. 1984 Jun;23(6):1011–1024. doi: 10.1002/bip.360230604. [DOI] [PubMed] [Google Scholar]
  2. Benevides J. M., Thomas G. J., Jr Characterization of DNA structures by Raman spectroscopy: high-salt and low-salt forms of double helical poly(dG-dC) in H2O and D2O solutions and application to B, Z and A-DNA. Nucleic Acids Res. 1983 Aug 25;11(16):5747–5761. doi: 10.1093/nar/11.16.5747. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Benevides J. M., Thomas G. J., Jr Characterization of DNA structures by Raman spectroscopy: high-salt and low-salt forms of double helical poly(dG-dC) in H2O and D2O solutions and application to B, Z and A-DNA. Nucleic Acids Res. 1983 Aug 25;11(16):5747–5761. doi: 10.1093/nar/11.16.5747. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Crawford J. L., Kolpak F. J., Wang A. H., Quigley G. J., van Boom J. H., van der Marel G., Rich A. The tetramer d(CpGpCpG) crystallizes as a left-handed double helix. Proc Natl Acad Sci U S A. 1980 Jul;77(7):4016–4020. doi: 10.1073/pnas.77.7.4016. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Dickerson R. E., Drew H. R., Conner B. N., Kopka M. L., Pjura P. E. Helix geometry and hydration in A-DNA, B-DNA, and Z-DNA. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):13–24. doi: 10.1101/sqb.1983.047.01.004. [DOI] [PubMed] [Google Scholar]
  6. Li Y., Thomas G. J., Jr, Fuller M., King J. Investigations of bacteriophage P22 by laser Raman spectroscopy. Prog Clin Biol Res. 1981;64:271–283. [PubMed] [Google Scholar]
  7. McIntosh L. P., Grieger I., Eckstein F., Zarling D. A., van de Sande J. H., Jovin T. M. Left-handed helical conformation of poly[d(A-m5C).d(G-T)]. Nature. 1983 Jul 7;304(5921):83–86. doi: 10.1038/304083a0. [DOI] [PubMed] [Google Scholar]
  8. Nishimura Y., Tsuboi M., Nakano T., Higuchi S., Sato T., Shida T., Uesugi S., Ohtsuka E., Ikehara M. Raman diagnosis of nucleic acid structure: sugar-puckering and glycosidic conformation in the guanosine moiety. Nucleic Acids Res. 1983 Mar 11;11(5):1579–1588. doi: 10.1093/nar/11.5.1579. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Prescott B., Steinmetz W., Thomas G. J., Jr Characterization of DNA structures by laser Raman spectroscopy. Biopolymers. 1984 Feb;23(2):235–256. doi: 10.1002/bip.360230206. [DOI] [PubMed] [Google Scholar]
  10. Thamann T. J., Lord R. C., Wang A. H., Rich A. The high salt form of poly(dG-dC).poly(dG-dC) is left-handed Z-DNA: Raman spectra of crystals and solutions. Nucleic Acids Res. 1981 Oct 24;9(20):5443–5457. doi: 10.1093/nar/9.20.5443. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Wang A. H., Fujii S., van Boom J. H., Rich A. Right-handed and left-handed double-helical DNA: structural studies. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):33–44. doi: 10.1101/sqb.1983.047.01.006. [DOI] [PubMed] [Google Scholar]
  12. Wang A. H., Quigley G. J., Kolpak F. J., Crawford J. L., van Boom J. H., van der Marel G., Rich A. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature. 1979 Dec 13;282(5740):680–686. doi: 10.1038/282680a0. [DOI] [PubMed] [Google Scholar]

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